I'm resurrecting this thread because I can't find an answer anywhere else on the forums and I have the same problem.
I have an Asus P6X58D motherboard with a Thermaltake ISGC400 fan, and I can't get the MB to control the fan speed. It sits at about 770 RPM or so. I've also tried the attachable manual knob, it appears to do nothing.
Testing with OCCT's CPU test, the fan speed doesn't increase but the temp does
. The test stops at 80 degrees. Also note my BIOS is 1501.